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Note: This is the first paper I wrote on the subject of horizontal gene transfer. It addresses the following subjects: why the genetic code is uniform, why von Baer's Law, parallelisms, and radiations in the fossil record.

Note: New posting September 6, 2012. This contains the first paper where the more theoretical aspects of horizontal gene transfer are outlined by the author. A major theme of this review is to make the case for mobile genetic elements and other mechanisms that promote horizontal gene transfer being shaped by the forces of natural selection via their ability to promote beneficial phenotypes. Or as has been said elsewhere: life has evolved to evolve.

Note: This is the first molecular evolution analysis I performed testing the hypothesis of horizontal gene transfer as a major force in evolution. This paper addresses whether or not neutral substitutions across the ß-globin gene are randomly distributed. It finishes with a theory as to the evolutionary function of introns.

Note: This paper presents a general discussion of the overall patterns of molecular evolution if horizontal gene transfer was a major force. It deals mostly with metazoan evolution from the point of view that viruses are major vectors of gene transfer.

Note: At the request of the late Allan C. Wilson, then editor of JME, we removed the discussion of horizontal gene transfer [ lateral gene transfer ] from this paper. Hence, I incorporated the discussion of the theoretical implications of this paper in a later review [ see below, paper 8 ]. The paper shows, as stated in the title, that homoplasy in plant evolution is more extensive than with animal evolution. And molecular data will not rescue the situation. With the accumulation of more recent plant sequences the problem of homoplasy remains.

Note: This is a short review of the book “Gene Transfer in the Environment”. It is included in this list because I explicitly address the issue of the whether the phenomena of reproductive isolation and the general pattern of nested hierarchies observed in taxonomy precludes a rate of horizontal gene transfer that could significantly influence macroevolutionary trends.

Note: This is a general review of horizontal gene transfer [ lateral gene transfer ] ... The main issue addressed here is how to identify a possible gene transfer event from comparative sequence analysis. This includes criteria for identification with many examples of artifactual identifications. This is includes an early review of those regions of bacterial chromosomes that are now called genomic islands and are central to understanding the concept of the pangenome. In addition, a case is made that angiosperm evolution is heavily influenced by horizontal gene transfer [ lateral gene transfer ].

Note: This paper is an extension of ideas presented in paper #1 on the unity of
the genetic code. A strong argument is presented that not only did the
genetic code continue to evolve after diversification of life's three major
kingdoms but that also the entity, commonly referred to as the Last Common
Ancestor, was actually a collection of disparate genetic lineages.

Reprinted at this web site with permission from Elsevier Science. The Trends in Genetics homepage is at: www.trends.com

10.

Michael Syvanen. 2002. On the Occurance of Horizontal Gene Transfer Among an Arbitrarily Chosen Group of 26 Genes. J. Mol. Evol. 54:258-266.

Note: This paper describes an analysis that began as an attempt to determine
which fraction of genes common to Bacteria, Archaea and Eukaryotes
supported the universal tree (Archaea and Eukaryotes as closest relatives)
as opposed to those that do not. In the course of the analysis, a group of
genes were selected that had high levels of similarity to each other --
this lead to a result that was initially surprising. Paper 8 was
originally the discussion for this paper, but the editors suggested it be
removed as being too speculative.

Note: This paper describes the distance matrix rate test, a tool that can be used
to illustrate horizontal gene transfer events (as shown in paper 10), but
otherwise does not address this topic. This paper ends with the suggestion
that the highly variable rates of evolution observed with the Eukaryotic
ribosomal RNA genes is a consequent of the hypothesized longevity sensor
that possibly resides in these genes.

Note: This paper is not available elsewhere through electronic
publishing. Ribosomal RNA sequences are used to obtain molecular distances
that are used to estimate divergence times. This work shows that many
major clades (angiosperm families and three metazoan groups) arose at times
significantly earlier than is indicated by the fossil record. This is
further evidence that major evolutionary radiations were possibly
accompanied by extensive horizontal gene transfers.

First Paragraph: It has been over 30 years since the suggestion that horizontal gene
transfer (HGT) may have been a factor in the evolution of life entered
the literature. Initially these speculations were based on discoveries
made in medical microbiology, namely, that genes for resistance to
antibiotics were found to move from one bacterial pathogen to another.
This discovery was so unexpected and contrary to accepted genetic
principles that though it was announced in Japan in 1959 [1,2], it was
not generally recognized in the West for another decade. Speculations
that HGT may have been a bigger factor in the evolution of life was
inviting because it offered broad explanations for a variety of biologi-
cal phenomena that have interested and puzzled biologists for over the
last century and a half, These were problems that had been raised by
botanists who have puzzled over the evolution of green plants 131 as
well as by paleontologists who recorded macroevolutionary trends [4]
in the fossil record that were often difficult to reconcile with the New
Synthesis that merged Darwin's thinking with Mendelian genetics.
However, outside of the field of bacteriology this exercise did not really
attract that much attention until the late 1990s, at which time there was
a major influx of data indicating that HGT had been very pervasive in
early life. Namely, complete genome sequences began to appear.
Simple examination of these sequences showed beyond any doubt that
horizontal gene transfer was indeed a major factor in the evolution of
modern bacterial, archaeal, and eukaryotic genomes.

Note: This paper is presented here with permission from "World Scientific Publishing Co. Pte. Ltd." They are the publisher and can be found at www.wspc.com.

Abstract: The availability of whole genome sequences from multiple metazoan phyla is making
it possible to determine their phylogeny. We have found that a sea urchin and human
define a clade that excludes a tunicate, contradicting both classical and recent molecular
studies that place the tunicate and vertebrate in the Chordate phylum. Intriguingly, by
means of a novel four taxa analysis, we have partitioned the 2000 proteins responsible
for this assignment into two groups. One group, containing about 40% of the proteins,
supports the classical assemblage of the tunicate with vertebrates, while the remaining
group places the tunicate outside of the chordate assemblage. The existence of these two
phylogenetic groups is robustly maintained in five, six and nine taxa analyses. These
results suggest that major horizontal gene transfer events occurred during the emergence
of one of the metazoan phyla. The simplest explanation is that the modern tunicate (as
represented by Ciona intestinalis) began as a hybrid between a primitive vertebrate and
some other organism, perhaps from an extinct and unidentified protostome phylum, at
a time close to but after the diversification of the chordates and echinoderms and before
the lineages leading to Drosophila melanogaster and Caenorhabditis elegans diverged.

Note: This latest review describes how horizontal gene transfer can change our thinking about such things as the tree of life, the notion of a last universal common ancestor,the biological unities, rules of taxonomic nomenclature, an unexpected support for Muller’s ratchet and the bacterial pangenome. The emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions.

Abstract: The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.

Note: The text for this note is being prepared by the author, Michael Syvanen.

Abstract: It is generally accepted that humans and sea urchins are deuterostomes and that fruit flies and jelly fish are outgroups. However, when we analyzed proteins from the genomes of these four species and submitted them to 4 taxa phylogenetic analysis, we found that, while as expected, most of the proteins (563) supported the notion of human and sea urchin in one clade and jelly fish and fruit flies in the other clade (Tree1), a large number of proteins (353) showed human and fruit fly in one clade with the sea urchin and jelly fish in the other (Tree3). Homologs were found in the genomes from 5 other metazoa. Tree1 proteins resulted in the expected 9 taxa tree, while the Tree3 proteins show vertebrates, to the exclusion of the other chordates, in the protostome clade. The two 9 taxa trees were fused into a single most parsimonious net that supports an introgression event between a vertebrate ancestor and a primitive protostome.

In 2002 Academic Press published a collection of reviews and original
research articles covering some of the most recent findings and insights
into horizontal gene transfer [ lateral gene transfer ]. This is editied by myself and Clarence Kado.

Horizontal gene transfer is the transfer of genetic material between distinct species, a process that plays a major role in the
evolution of the genome. Evidence for the transfer of genes singly and in modular groups between lower and higher organisms
(including humans) has been mounting. The second edition of Horizontal Gene Transfer [ lateral gene transfer ] has been organized to provide a
concise and up-to-date coverage of the most important discoveries in this fascinating field. Written by the most prominent gene
transfer and genome analytical scientists, this book details experimental evidence for the phenomenon of horizontal gene transfer [ lateral gene transfer ]
and discusses further evidence provided by the recent completion of genomic sequences from Archea, Bacteria, and Eucarya
members.